Run ID: SRR13861138
Sample name:
Date: 03-04-2023 09:24:26
Number of reads: 648825
Percentage reads mapped: 10.82
Strain: lineage4.9
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761131 | p.Gly442Glu | missense_variant | 0.26 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5624 | p.Asn129Asp | missense_variant | 1.0 |
gyrA | 7541 | c.240C>G | synonymous_variant | 0.11 |
mshA | 575194 | c.-154G>T | upstream_gene_variant | 1.0 |
rpoB | 760907 | c.1101_1102insT | frameshift_variant | 1.0 |
rpoB | 761102 | c.1296A>G | synonymous_variant | 0.17 |
rpoB | 761126 | c.1320G>T | synonymous_variant | 0.27 |
rpoB | 761129 | c.1323G>C | synonymous_variant | 0.26 |
rpoB | 761133 | p.Leu443Ile | missense_variant | 0.28 |
rpoB | 761150 | c.1344A>C | synonymous_variant | 0.3 |
rpoB | 761151 | p.Leu449Val | missense_variant | 0.27 |
rpoB | 761156 | c.1350G>C | synonymous_variant | 0.27 |
rpoB | 761162 | c.1356G>C | synonymous_variant | 0.26 |
rpoB | 761165 | c.1359G>C | synonymous_variant | 0.29 |
rpoB | 761168 | c.1362C>G | synonymous_variant | 0.29 |
rpoB | 761178 | p.Ser458Thr | missense_variant | 0.27 |
rpoB | 761192 | c.1386C>G | synonymous_variant | 0.25 |
rpoB | 761195 | c.1389G>C | synonymous_variant | 0.26 |
rpoB | 761196 | p.Leu464Phe | missense_variant | 0.26 |
rpoB | 761204 | c.1398C>T | synonymous_variant | 0.29 |
rpoB | 761207 | c.1401C>T | synonymous_variant | 0.29 |
rpoB | 761213 | c.1407G>A | synonymous_variant | 0.27 |
rpoB | 761220 | p.Ser472Thr | missense_variant | 0.28 |
rpoB | 761234 | c.1428G>C | synonymous_variant | 0.28 |
rpoB | 761235 | p.Met477Val | missense_variant | 0.28 |
rpoB | 762878 | p.Ile1024Met | missense_variant | 0.21 |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.21 |
rpoB | 762888 | p.His1028Asn | missense_variant | 0.19 |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.22 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.23 |
rpoC | 762929 | c.-441G>C | upstream_gene_variant | 0.24 |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.23 |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.22 |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.21 |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.21 |
rpoC | 762962 | c.-408C>T | upstream_gene_variant | 0.23 |
rpoC | 762971 | c.-399G>A | upstream_gene_variant | 0.25 |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.31 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.33 |
rpoC | 762995 | c.-375G>T | upstream_gene_variant | 0.33 |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.14 |
rpoC | 764401 | c.1032C>T | synonymous_variant | 0.17 |
rpoC | 764404 | c.1035C>T | synonymous_variant | 0.17 |
rpoC | 764405 | c.1036A>C | synonymous_variant | 0.17 |
rpoC | 764419 | c.1050C>T | synonymous_variant | 0.17 |
rpoC | 764428 | c.1059G>T | synonymous_variant | 0.17 |
rpoC | 764434 | c.1065A>G | synonymous_variant | 0.17 |
rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.17 |
rpoC | 764441 | p.Ile358Leu | missense_variant | 0.13 |
rpoC | 764446 | c.1077T>C | synonymous_variant | 0.17 |
rpoC | 764451 | p.Gly361Ala | missense_variant | 0.17 |
rpoC | 764455 | c.1086G>T | synonymous_variant | 0.17 |
rpoC | 764461 | p.Glu364Asp | missense_variant | 0.17 |
rpoC | 764470 | c.1101C>G | synonymous_variant | 0.17 |
rpoC | 764471 | p.Asn368Arg | missense_variant | 0.17 |
rpoC | 764479 | c.1110G>A | synonymous_variant | 0.17 |
rpoC | 764485 | c.1116G>C | synonymous_variant | 0.16 |
rpoC | 764498 | p.Ser377Ala | missense_variant | 0.19 |
rpoC | 764503 | c.1134G>C | synonymous_variant | 0.19 |
rpoC | 764509 | c.1140G>C | synonymous_variant | 0.19 |
rpoC | 764513 | p.Phe382Leu | missense_variant | 0.21 |
rpoC | 764521 | c.1152T>C | synonymous_variant | 0.25 |
rplC | 801226 | p.Gly140Arg | missense_variant | 1.0 |
embR | 1417503 | c.-156A>C | upstream_gene_variant | 1.0 |
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.46 |
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.46 |
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.46 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.48 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.91 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476753 | n.3099delG | non_coding_transcript_exon_variant | 1.0 |
fabG1 | 1673233 | c.-207T>G | upstream_gene_variant | 1.0 |
rpsA | 1833593 | c.53delC | frameshift_variant | 1.0 |
rpsA | 1834884 | p.Gln448Leu | missense_variant | 1.0 |
PPE35 | 2169282 | p.Arg444His | missense_variant | 1.0 |
ahpC | 2725932 | c.-261G>A | upstream_gene_variant | 1.0 |
pepQ | 2859739 | p.Ala227Gly | missense_variant | 1.0 |
pepQ | 2860197 | c.222T>C | synonymous_variant | 1.0 |
Rv3083 | 3448909 | p.Leu136Ile | missense_variant | 1.0 |
fbiA | 3640691 | p.Asp50Val | missense_variant | 1.0 |
fbiA | 3641204 | p.Gly221Asp | missense_variant | 1.0 |
clpC1 | 4039961 | p.Tyr248* | stop_gained | 1.0 |
embC | 4240818 | p.Thr319Arg | missense_variant | 1.0 |
embB | 4248081 | c.1569dupG | frameshift_variant | 1.0 |
ethA | 4327644 | c.-171G>A | upstream_gene_variant | 1.0 |